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From: Scott C. <no...@gi...> - 2023-04-10 16:37:33
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Branch: refs/heads/master Home: https://github.com/GMOD/GBrowse Commit: 528effccfcbed1c77c542c1536679425263e489b https://github.com/GMOD/GBrowse/commit/528effccfcbed1c77c542c1536679425263e489b Author: Scott Cain <sco...@sc...> Date: 2023-04-10 (Mon, 10 Apr 2023) Changed paths: M README Log Message: ----------- Update README |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:52:16
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Branch: refs/heads/release_1_62 Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:46:30
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Branch: refs/heads/release-2_09 Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:30:57
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Branch: refs/heads/imagemap_pull Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:30:57
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Branch: refs/heads/test-wig-upload Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:30:57
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Branch: refs/heads/aws-slave-grow-vol Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:30:37
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Branch: refs/heads/security-bug-fixes Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:30:37
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Branch: refs/heads/transparency Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:30:35
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Branch: refs/heads/scotts-minor-fixes Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:30:34
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Branch: refs/heads/pinned-tracks-2 Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:36
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Branch: refs/heads/security-bug-fixes Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:35
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Branch: refs/heads/scotts-minor-fixes Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:29
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Branch: refs/heads/pinned-tracks-2 Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:27
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Branch: refs/heads/aws-slave-grow-vol Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:24
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Branch: refs/heads/transparency Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:22
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Branch: refs/heads/imagemap_pull Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:18
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Branch: refs/heads/test-wig-upload Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:29:12
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Branch: refs/heads/release-2_09 Home: https://github.com/GMOD/GBrowse |
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From: Nathan W. <no...@gi...> - 2022-08-10 22:28:59
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Branch: refs/heads/release_1_62 Home: https://github.com/GMOD/GBrowse |
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From: Nathan T. W. <we...@ia...> - 2018-04-06 18:10:33
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Branch: refs/heads/master Home: https://github.com/GMOD/GBrowse Commit: 24834fb7ad5e159a65e1f76f317963090bf64cc0 https://github.com/GMOD/GBrowse/commit/24834fb7ad5e159a65e1f76f317963090bf64cc0 Author: Mark Heiges <mh...@ug...> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/Bio/Graphics/Browser2/Render.pm Log Message: ----------- CGI escape track list in URIs Commit: 28ad7c5d60b0eed8682794470229ad64a525f19a https://github.com/GMOD/GBrowse/commit/28ad7c5d60b0eed8682794470229ad64a525f19a Author: Mark Heiges <mh...@ug...> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/Bio/Graphics/Browser2/Render.pm Log Message: ----------- fix double escaping of delimiter that was breaking the 'Generate URL' feature Commit: f0c7ec1c7640c79585e32d1ef8bacb5ed5de70a7 https://github.com/GMOD/GBrowse/commit/f0c7ec1c7640c79585e32d1ef8bacb5ed5de70a7 Author: Mark Heiges <mh...@ug...> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M lib/Bio/Graphics/Browser2/Render.pm Log Message: ----------- cleanup extraneous/invalid parentheses Commit: 116a7dfeb1d8ecd524cdeebdc1c1a760938a2fd0 https://github.com/GMOD/GBrowse/commit/116a7dfeb1d8ecd524cdeebdc1c1a760938a2fd0 Author: Nathan T. Weeks <we...@ia...> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/Bio/Graphics/Browser2/Render.pm Log Message: ----------- Merge pull request #62 from mheiges/svgexport Fixes internal server error on SVG & PNG export introduced by fix for CVE-2016-87430 in Apache 2.4.26 Compare: https://github.com/GMOD/GBrowse/compare/8c2f027885f1...116a7dfeb1d8 |
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From: Arna G. <arn...@ma...> - 2018-02-07 02:07:04
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Hello, I was trying to install the latest version of GBrowse2 (I followed the steps mentioned in the "Install manually" section of http://gmod.org/wiki/GBrowse_2.0_Install_HOWTO) with Perl 2.56 on Ubuntu 17.10. However after I install GBrowse, when I try viewing the "Yeast chromosomes 1+2 (basic)" which is provided in the database (I assume), it throws the error "Attempt to reload Bio/DB/SeqFeature/Store/memory.pm aborted. Compilation failed in require. at /usr/local/lib/x86_64-linux-gnu/perl/5.26.0/Bio/Graphics/Browser2/DataBase.pm line 46." on the top of the webpage in red. Although the page shows up with all the formatting correct, it doesn't show any chromosome when I click on example "landmarks/regions". The log file for Apache also shows me a similar error message and I presume it refers to the error in loading the database. Could somebody point me to where the bug could lie and what I should do to fix it. Also, once I install the webpage is always hosted on localhost. If I want to reinstall GBrowse, do I need to stop the localhost and then reinstall? Could somebody point me to steps for doing that. Thank you so much. Regards Arna Ghosh |
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From: lstein <lin...@gm...> - 2017-01-15 21:17:11
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Branch: refs/tags/release-2.56 Home: https://github.com/GMOD/GBrowse |
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From: Lincoln S. <lin...@gm...> - 2017-01-15 21:16:50
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Branch: refs/heads/master Home: https://github.com/GMOD/GBrowse Commit: 8c2f027885f155cb5b8d5fd8d09a62e05996f16a https://github.com/GMOD/GBrowse/commit/8c2f027885f155cb5b8d5fd8d09a62e05996f16a Author: Lincoln Stein <lin...@gm...> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M Build.PL M README Log Message: ----------- In-memory adaptor requires perl 1.007001 to run -- added this to README and prerequisites |
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From: Lincoln S. <ls...@ls...> - 2017-01-15 20:04:26
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Branch: refs/heads/master Home: https://github.com/GMOD/GBrowse Commit: 9a2327e009ca0a014f0d14ac3dc9afd26bbe081f https://github.com/GMOD/GBrowse/commit/9a2327e009ca0a014f0d14ac3dc9afd26bbe081f Author: Lincoln Stein <lin...@gm...> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/Bio/Graphics/Browser2/Action.pm M lib/Bio/Graphics/Browser2/DataSource.pm M lib/Bio/Graphics/Browser2/Render.pm Log Message: ----------- fixed perl 5.22.1 deprecations and CGI param() list context warnings Commit: b11d2c57f4bf30bc35ded60ed1c62b88fa8ce6a9 https://github.com/GMOD/GBrowse/commit/b11d2c57f4bf30bc35ded60ed1c62b88fa8ce6a9 Author: Lincoln Stein <lin...@gm...> Date: 2016-12-29 (Thu, 29 Dec 2016) Changed paths: M htdocs/js/login.js M lib/Bio/Graphics/Browser2/Render.pm M lib/Bio/Graphics/Browser2/Render/Login.pm M lib/Bio/Graphics/Browser2/SendMail.pm M lib/Bio/Graphics/Browser2/UserDB.pm Log Message: ----------- fixed security bug which allowed an anonymous user to delete another user's account Commit: 8178e9ab3aaaadccd63dde4a73bce9991f2dc0eb https://github.com/GMOD/GBrowse/commit/8178e9ab3aaaadccd63dde4a73bce9991f2dc0eb Author: Scott Cain <sco...@sc...> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/Bio/Graphics/Browser2/Render.pm M lib/Bio/Graphics/Browser2/Render/Slave.pm Log Message: ----------- addition of CGI::multi_param to silence warnings when running tests--not sure if this is the right thing to do from a security perspective though (for example, should some of these calls be in a scalar context instead?) Commit: 361556a32c740166967efdfa1ffa69503922cbda https://github.com/GMOD/GBrowse/commit/361556a32c740166967efdfa1ffa69503922cbda Author: Lincoln Stein <lin...@gm...> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M lib/Bio/Graphics/Browser2/Render.pm M lib/Bio/Graphics/Browser2/Render/Slave.pm Log Message: ----------- Merge pull request #59 from GMOD/scotts-minor-fixes addition of CGI::multi_param to silence warnings when running tests--… Commit: c3d34bb28a7d4a4c88120b007ec6732f95c5dbb0 https://github.com/GMOD/GBrowse/commit/c3d34bb28a7d4a4c88120b007ec6732f95c5dbb0 Author: Lincoln Stein <ls...@ls...> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M htdocs/js/login.js M lib/Bio/Graphics/Browser2/Action.pm M lib/Bio/Graphics/Browser2/DataSource.pm M lib/Bio/Graphics/Browser2/Render.pm M lib/Bio/Graphics/Browser2/Render/Login.pm M lib/Bio/Graphics/Browser2/Render/Slave.pm M lib/Bio/Graphics/Browser2/SendMail.pm M lib/Bio/Graphics/Browser2/UserDB.pm Log Message: ----------- Merge remote-tracking branch 'origin/security-bug-fixes' Commit: 61c04309926c2e7536c9d7f85842a81416713400 https://github.com/GMOD/GBrowse/commit/61c04309926c2e7536c9d7f85842a81416713400 Author: Lincoln Stein <ls...@ls...> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M Changes M lib/Bio/Graphics/Browser2.pm Log Message: ----------- Bump version to 2.56 - still needs testing Compare: https://github.com/GMOD/GBrowse/compare/9aaeeb9fd33f...61c04309926c |
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From: Lincoln S. <lin...@gm...> - 2017-01-15 19:41:37
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Branch: refs/heads/master Home: https://github.com/GMOD/GBrowse Commit: 460baf150d268c85c004b532f0998434b3e12347 https://github.com/GMOD/GBrowse/commit/460baf150d268c85c004b532f0998434b3e12347 Author: Nathan T. Weeks <nat...@ar...> Date: 2015-03-04 (Wed, 04 Mar 2015) Changed paths: M lib/Bio/Graphics/Browser2/Render/HTML.pm Log Message: ----------- Left-align citation text in "?" menu. Commit: 9aaeeb9fd33f2020877c10ae74077d47a588664e https://github.com/GMOD/GBrowse/commit/9aaeeb9fd33f2020877c10ae74077d47a588664e Author: Lincoln Stein <lin...@gm...> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M lib/Bio/Graphics/Browser2/Render/HTML.pm Log Message: ----------- Merge pull request #50 from nathanweeks/issue/left-align-citation Left-align citation text in "?" menu. Compare: https://github.com/GMOD/GBrowse/compare/3100bb4f800c...9aaeeb9fd33f |
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